[gmx-users] problem

[Justin Lemkul]

On 9/22/18 2:31 AM, Alex wrote:
> Actually, I'd like to know, too. I keep seeing this warning for systems
> that are fully described in their topologies and all parameters
> appropriately present in ffnonbonded, etc, i.e. everything passes grompp
> and runs perfectly fine. I never really paid much attention to this
> warning, thinking that gmx solvate has its own way of looking things up
> elsewhere, but an explanation would be nice. I searched the list, but only
> found reference to the -shell option, which I am not using.
>
> What's happening?

This generic warning shows up for any program that uses atomic radii but 
has not been provided a .tpr file, which contains unambiguous masses and 
atom types. The warning just alerts the user to the possibility that 
something strange might happen when guessing what an atom is based 
solely on its name. For example, "CA" is often the alpha-carbon in 
proteins, but could it be a calcium ion in some cases? Similarly, is 
"HG" a hydrogen at the gamma-position or is it mercury?

-Justin

> Thanks,
>
> Alex
>
>
> On Sat, Sep 22, 2018 at 12:14 AM AKANXA TIWARI <akanxatiwari24 at gmail.com>
> wrote:
>
>> hello
>> i am simulating tubulin heterodimer . after giving command for solvent
>> adding i got a warning on screen what should i do.
>>
>> Initialising inter-atomic distances...
>>
>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>>           based on residue and atom names, since they could not be
>>           definitively assigned from the information in your input
>>           files. These guessed numbers might deviate from the mass
>>           and radius of the atom type. Please check the output
>>           files if necessary.
>>
>> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
>> from the source below. This means the results may be different
>> compared to previous GROMACS versions.
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> A. Bondi
>> van der Waals Volumes and Radii
>> J. Phys. Chem. 68 (1964) pp. 441-451
>> -------- -------- --- Thank You --- -------- --------
>>
>> Generating solvent configuration
>> Will generate new solvent configuration of 7x7x7 boxes
>> Solvent box contains 202791 atoms in 67597 residues
>> Removed 17799 solvent atoms due to solvent-solvent overlap
>> Removed 10800 solvent atoms due to solute-solvent overlap
>> Sorting configuration
>> Found 1 molecule type:
>>      SOL (   3 atoms): 58064 residues
>> Generated solvent containing 174192 atoms in 58064 residues
>> Writing generated configuration to 1jff_solv.gro
>>
>> Output configuration contains 182636 atoms in 58902 residues
>> Volume                 :     1882.42 (nm^3)
>> Density                :     1006.94 (g/l)
>> Number of solvent molecules:  58064
>>
>> Processing topology
>> Adding line for 58064 solvent molecules with resname (SOL) to topology file
>> (topol.top)
>>
>> Back Off! I just backed up topol.top to ./#topol.top.1#
>>
>> GROMACS reminds you: "She's Not Bad, She's Just Genetically Mean" (Captain
>> Beefheart)
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================